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发表于 2008-9-1 22:15
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Theoretical Biophysics Lecture note(2007)
Theoretical Biophysics
http://wwwcp.tphys.uni-heidelberg.de/biophysics/index.php
Prerequisits:
Basic knowledge in Classical Mechanics, Electrodynamics and Statistical Mechanics
Abstract
The emergence of new cross-disciplinary fields is one of the major driving forces in science and technology. Among the most important of these emerging fields are those which connect the life sciences with physics. Due to the vast amount of data that is now available there is the possibility to understand living organisms as complex dynamic systems. Biological processes occur on a wide range of spatial and temporal scales. The time scales of biological function range from very fast femtosecond molecular motions, to multi second protein folding pathways, to cell cycle and development processes that take place over the order of minutes, hours and days. Similarly, the dimensions of biological interest range from small organic molecules to multi-protein complexes, to cellular processes, to tissues, to the interaction of human populations with the environment. Thus one needs to understand how on the smallest scale conformational changes of molecules plus their interaction give rise to collective phenomena.
Lecture notes:
• Week 1 (new version Mai 5, 2006, only a very minor modification with respect to the April version): Freely jointed chain, contour length, end-to-end distance, radius of gyration, Kuhn segment length, persistence length, lattice chains
• Week 2 (new version Mai 5, 2006): Gaussian chain model, Worm-like chain model, relation to Heisenberg model
• Week 3 (new version Mai 12, 2006): Self avoiding random walk, n-vector model, energy landscape, random heteropolymer, REM model, glas transition temperature
• Week 4 (new version Mai 17, 2006): macromolecules in solution, Flory-Huggins theory, theta-temperature, phase transitions, intermolecular potentials, electrostatic screening, helix-coil transition
• Week 5: helix-coil transition, Zimm Bragg model, DNA melting, Poland-Scheraga-model, Kittel zipper-model
• Week 6: polyelectrolytes, Poisson-Boltzmann equation, Debye-screening length, Bjerrum length, Manning parameter, protein, primary structure, secondary structure, beta-sheets, tertiary structure, force fields
• Week 7: protein folding, numerical methods, Molecular Dynamics, Langevin Dynamics, Monte Carlo
• Week 8: Lattice models, HP-model, LS-model, designability of proteins, spin-glas, pivot-algorithm, simulated annealing, chromatin, two-angle model, phase diagram for chromatin
• Week 9: Membranes, surfaces, random surface, curvature, bending rigdity, Hausdorff dimension, phase transition
• Week 10: Recap
• Week 11 (new version July 1, 2006): Macromolecular dynamics, diffusion, Hydrodynamics, Rouse dynamics
• Week 12 (new version July 4, 2006): Networked systems, gel, Flory-Stockmayer theory, percolation, site percolation, bond percolation, electrophoresis
• Week 13: Bayesian inference, Bayesian networks, gene regulatory networks, random boolean network
• Week 14: Here are some online references to further online material concerning networks
o Learning bayesian networks with R
o Bayesian network models for gene regulation
o Analysis and comprehension of genomic data
• Bibliography and key word list (Version Mai 5, 2006): Will be updates continuously and may not match with the reference number in the notes at this stage!
The full script version (but still very sketchy). Return frequently for an updated version.
Contents:
1. Introduction
2. Macromolecules
o General Properties of Macromolecules
Freely jointed chain
The Gaussian chain model
Elastic rod model
Self Avoiding Chains
Conformations and Energy Lanscapes
Macromolecules in Solution
Macromolecules at a Surface
o Intermolecular interactions and electrostatic screening
o Helix-Coil Transition
o DNA Melting
o Polyelectrolytes
The Poisson-Boltzmann equation
o Proteins
Protein folding
Numerical approaches
Folding as a spin glass problem
Protein-protein interactions
o Chromatin
Chromatin Models
Force-extension behavior of folded macromolecules
o Genes
Gene expression and genetic code
3. Membranes
o Self–assembly of micelles
o Surface Behavior of Lipids
Differential geometry of surfaces
Membrane elasticity and bending energy
Membrane fluctuations
o Structure of Lipids
o Cell Membranes
4. Transport
o Diffusion
o Polymer dynamics
Rouse Model
Hydrodynamic interactions
Reptation
5. Networks
o Gels
o Metabolic Networks
Boolean Networks
Scale-free Networks
Robustness of Networks
6. Molecular Motors
o Polymerization of cell filaments
o Brownian ratchet
o A basic model of a molecular motor
7. Statistical Analysis
o A first example
o Bayesian Analysis
o Monte Carlo Methods
o Hidden Markov Models
Literature:
• Harvey Lodish, Arnold Berk, Paul Matsudaira, Molecular Cell Biology, W.H. Freeman and Co, ISBN: 071676152, 5th Edition 2004
• Philip Nelson, Biological Physics: Energy, Information, Life, Publisher: W H Freeman and Co, 2003
• P. Nelson, Biological physics, W.H.Freeman, 2004
• David Boal, Mechanics of the Cell, Cambridge University Press, 2002.
• Roland Glaser, Biophysics, New York : Springer, 2001.
• Rodney Cotterill, Biophysics : An introduction, Chichester ; New York : Wiley, 2002
© 2007 Dieter W. Heermann |
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